Appointed in May 2010, the 39-year-old steered the Blues to unprecedented success, guiding them to three successive league titles and back into non-league’s elite.
But this season has presented unfamiliar difficulties and, with Chester battling relegation, Young told The Chronicle the time was right to move on.
“I love a cliche and all good things must come to an end at some time,” he said.
“I’m very proud to have been given the opportunity to manage such a fantastic club and the memories of the last three years will live with me forever.”
Young left Colwyn Bay to join the reborn Blues and found a club with no kits, no equipment and lacking the most basic infrastructure.
Together with the board and volunteers, Young set about building the club from the bottom up.
“To start a club with nothing and three years later be in the Conference Premier, to break so many records and win so many awards has been amazing,” he said.
“I have had some fantastic times and it’s a massive credit to everybody involved to have got the club to where it is today.
“We have been on an amazing journey together. If we could go back in time and do it all again then I’m sure that we would.”
Young plans to take a break from the game and spend more time with his wife and two young daughters.
“From the start I have put so much time into Chester and I am grateful to my family for allowing me to do that,” he said.
“It’s the first time in 14 years I have been out of football and I have made a lot of sacrifices and my kids have got their dad back now.”
Young’s best friend Gary Jones steps up from his role as assistant manager to become caretaker boss as the club begins the search for his successor with Saturday the deadline for applications.
Former Chester City boss Jim Harvey has been helping the club look into setting up a new youth side and would appear an obvious replacement.
However, he told The Chronicle he had no interest in the role.
“It’s not something I’m interested in and I would not be pursuing that,” he said.
“I am very fond of the club and I have a lot of friends there. I wish Neil Young the best and will do the same to anybody who comes in.”
Possible contenders include sacked Kidderminster Harriers boss Steve Burr and ex-Luton Town manager Gary Brabin.
Airbus UK boss Andy Preece and former Chester City defender Iain Jenkins, now working for the Scottish FA, could also be keen.
“The players are going to need the fans behind them more than ever and so is the new gaffer," said Young.
“I hope I always have a fantastic relationship with the supporters and I’m very proud I can walk away from the club with this legacy.”